Thermodynamic analysis of biomolecular interactions

A Multi-Spectroscopic and Molecular Docking Analysis of the Biophysical Interaction between Food Polyphenols, Urolithins, and Human Serum Albumin

Secondary polyphenol metabolites, urolithins (UROs), have anti-oxidative, anti-inflammatory, and antidiabetic properties. Therefore, their biological activity relies on blood transport via human serum albumin (HSA) and tissue distribution. The main goal we set was to investigate the interaction between HSA and different URO (URO A, URO B, URO C, URO D, and glucuronidated URO A and B) using a combination of multi-spectroscopic instrumental and in silico approaches. The fluorescence spectroscopy revealed that URO can quench the naturally occurring fluorescence of HSA in a concentration-dependent manner. The HSA fluorescence was quenched by both a static and dynamic mechanism. The results showed that free UROs bind to HSA with higher affinity than their conjugated forms. CD spectroscopy and FTIR revealed that the alpha-helical structure of HSA is preserved. The calculated Gibbs free energy change indicates that the URO-HSA complex forms spontaneously. There is a single binding site on the HSA surface. The molecular docking results indicated that unconjugated Uro binds to Sudlow I, while their conjugation affects this binding site, so in the conjugated form, they bind to the cleft. Docking experiments indicate that all UROs are capable of binding to both thyroxine recognition sites of ligand-bound HSA proteins. Examining interactions under the following conditions (298 K, 303 K, and 310 K, pH 7.4) is of great importance for determining the pharmacokinetics of these bioactive compounds, as the obtained results can be used as a basis for modulating the potential dosing regimen.

Zeta potential of Z-DNA: A new signature to study B-Z transition in linear and branched DNA

Zeta potential is commonly referred as surface charge density and is a key factor in modulating the structural and functional properties of nucleic acids. Although the negative charge density of B-DNA is well understood, there is no prior description of the zeta potential measurement of Z-DNA. In this study, for the first time we discover the zeta potential difference between B-DNA and lanthanum chloride-induced Z-DNA. A series of linear repeat i.e. (CG)n and (GC)n DNA as well as branched DNA (bDNA) structures was used for the B-to-Z DNA transition. Herein, the positive zeta potential of Z-DNA has been demonstrated as a powerful tool to discriminate between B-form and Z-form of DNA. The generality of the approach has been validated both in linear and bDNA nanostructures. Thus, we suggest zeta potential can be used as an ideal signature for the left-handed Z-DNA.

It's Time for Entropic Clocks: The Roles of Random Chain Protein Sequences in Timing Ion Channel Processes Underlying Action Potential Properties

In recent years, it has become clear that intrinsically disordered protein segments play diverse functional roles in many cellular processes, thus leading to a reassessment of the classical structure-function paradigm. One class of intrinsically disordered protein segments is entropic clocks, corresponding to unstructured random protein chains involved in timing cellular processes. Such clocks were shown to modulate ion channel processes underlying action potential generation, propagation, and transmission. In this review, we survey the role of entropic clocks in timing intra- and inter-molecular binding events of voltage-activated potassium channels involved in gating and clustering processes, respectively, and where both are known to occur according to a similar 'ball and chain' mechanism. We begin by delineating the thermodynamic and timing signatures of a 'ball and chain'-based binding mechanism involving entropic clocks, followed by a detailed analysis of the use of such a mechanism in the prototypical Shaker voltage-activated K+ channel model protein, with particular emphasis on ion channel clustering. We demonstrate how 'chain'-level alternative splicing of the Kv channel gene modulates entropic clock-based 'ball and chain' inactivation and clustering channel functions. As such, the Kv channel model system exemplifies how linkage between alternative splicing and intrinsic disorder enables the functional diversity underlying changes in electrical signaling.

Differential scanning calorimetry (DSC) as a tool for studying thermal properties of a crude cellulase cocktail

Abstract

Differential scanning calorimetry (DSC) was used as an efficient and rapid tool in studying the conformational transitions between the folded and unfolded structures of cellulolytic enzymes. The thermal properties of two crude hydrolytic enzyme cocktails containing extracellular cellulases from Trichoderma longibrachiatum DIBAF-10 were analyzed and compared with three commercial cellulase preparations. Differences in the thermal behavior of fungal cellulases in the liquid phase, freeze-dried state, liquid formulations in sodium citrate buffer (pH 4.8), and contact with cellulose, carboxymethyl cellulose, and cellobiose were evaluated. DSC profiles of cellulases from the DIBAF-10 strain provided important thermodynamic information about the thermal stability of the included proteins. Crude enzyme cocktails underwent a reproducible and irreversible exothermic aggregation phenomenon at 52.45 ± 0.90 °C like commercial β-glucosidase. Freeze-dried and resuspended in a sodium citrate buffer, cellulases from T. longibrachiatum showed an endothermic peak dependent on buffer and enzyme concentration. In the enzyme-substrates systems, a shift of the same peak was recorded for all substrates tested. The thermal analysis of freeze-dried cellulase samples in the range of 20–150 °C gave information on the denaturation process. In conclusion, we demonstrated that DSC is a cost-effective tool for obtaining "conformational fingerprinting" of crude fungal cellulase preparations.

Graphical abstract

The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction

The nucleoplasmin family of histone chaperones is a key player in governing the dynamic architecture of chromatin, thereby regulating various DNA-templated processes. The crystal structure of the N-terminal domain of Arabidopsis thaliana FKBP43 (AtFKBP43), an FK506-binding immunophilin protein, revealed a characteristic nucleoplasmin fold, thus confirming it to be a member of the FKBP nucleoplasmin class. Small-Angle X-ray Scattering (SAXS) analyses confirmed its pentameric nature in solution, and additional studies confirmed the nucleoplasmin fold to be highly stable. Unlike its homolog AtFKBP53, the AtFKBP43 nucleoplasmin core domain could not interact with histones and required the acidic arms, C-terminal to the core, for histone association. However, SAXS generated low-resolution envelope structure, ITC, and AUC results revealed that an AtFKBP43 pentamer with C-terminal extensions interacts with H2A/H2B dimer and H3/H4 tetramer in an equimolar ratio, like AtFKBP53. Put together, AtFKBP43 belongs to a hitherto unreported subclass of FKBP nucleoplasmins that requires the C-terminal acidic stretches emanating from the core domain for histone interaction.

Biophysical interaction between lanthanum chloride and (CG)n or (GC)n repeats: A reversible B-to-Z DNA transition

The transition from right-handed to left-handed DNA is not only acts as the controlling factor for switching gene expression but also has equal importance in designing nanomechanical devices. The (CG)_n and (GC)_n repeat sequences are well known model molecules to study B-Z transition in the presence of higher concentration of monovalent cations. In this communication, we report a cyclic transition in (CG)₆ DNA using millimolar concentration of trivalent lanthanide salt LaCl₃. The controlled and reversible transition was seen in (CG)₁₂, and (GC)₁₂ DNA employing CD spectroscopy. While LaCl₃ failed to induce B-Z transition in shorter oligonucleotides such as (CG)₃ and (GC)₃, a smooth B-Z transition was recorded for (CG)₆, (CG)₁₂ and (GC)₁₂ sequences. Interestingly, the phenomenon was reversible (Z-B transition) with addition of EDTA. Particularly, two rounds of cyclic transition (B-Z-B-Z-B) have been noticed in (CG)₆ DNA in presence of LaCl₃ and EDTA which strongly suggest that B-Z transition is reversible in short repeat sequences. Thermal melting and annealing behaviour of B-DNA are reversible while the thermal melting of LaCl₃-induced Z-DNA is irreversible which suggest a stronger binding of LaCl₃ to the phosphate backbone of Z-DNA. This was further supported by isothermal titration calorimetric study. Molecular dynamics (MD) simulation indicates that the mode of binding of La³⁺ (of LaCl₃) with d(CG)₈.d(CG)₈ is through the minor groove, wherein, 3 out of 11 La³⁺ bridge the anionic oxygens of the complementary strands. Such a tight coordination of La³⁺ with the anionic oxygens at the minor groove surface may be the reason for the experimentally observed irreversibility of LaCl₃-induced Z-DNA seen in longer DNA fragments. Thus, these results indicate LaCl₃ can easily be adopted as an inducer of left-handed DNA in other short oligonucleotides sequences to facilitate the understanding of the molecular mechanism of B-Z transition.

Effects of zinc binding on the binding of epigallocatechin gallate (green tea) to bovine serum albumin and myoglobin

Serum albumin as a zinc carrier binds 80% plasma zinc to facilitate zinc absorption. Epigallocatechin gallate (EGCG, green tea) is reported to bind to serum albumin to perform its biological functions in vivo. However, the available information on how zinc binding affects the binding of EGCG to proteins or how EGCG binding affects the binding of zinc to proteins are very limited. In the present study, the effects of zinc binding on the binding of EGCG to bovine serum albumin and myoglobin were investigated using isothermal titration calorimetry, fluorescence quenching and molecular docking. The obtained results suggested that binding of zinc to bovine serum albumin and myoglobin could increase the EGCG binding affinity of proteins as indicated by the thermodynamic parameters. In addition, the formation of protein/zinc complex shifted the EGCG binding site of proteins. For myoglobin, the electron transfer from EGCG to myoglobin was facilitated by zinc binding induced stronger EGCG binding to myoglobin. Such study provides very fundamental and useful knowledge for zinc and EGCG nutrition.

Molecular binding interaction of pyridinium based gemini surfactants with bovine serum albumin: Insights from physicochemical, multispectroscopic, and computational analysis

To study the interaction of the series of pyridinium based gemini surfactants (GS) (referred to as m-Py-m, m = 14, 16); 4,4'-(propane-1,3-diyl)bis(1-(2-(tetradecyloxy)-2-oxoethyl) dipyridinium chloride (14-Py-14), and 4,4'-(propane-1,3-diyl) bis(1-(2-(hexadecyloxy)-2-oxoethyl)dipyridinium chloride (16-Py-16) with bovine serum albumin (BSA), various physicochemical and spectroscopic tools such as tensiometry, steady-state fluorescence, synchronous fluorescence, pyrene fluorescence, UV-visible, far-UV circular dichroism (CD) were utilized at physiological pH (7.4) and 298 K in combination with computational molecular modeling analysis. The tensiometric results show significant modifications in interfacial and thermodynamic parameters for m-Py-m GS upon BSA combination, deciphering the gemini surfactant-BSA interaction. Steady-state fluorescence analysis evaluates the structural alterations of BSA with the addition of m-Py-m GS. The plots of Stern-Volmer, modified Stern-Volmer, and thermodynamic parameters were used to determine the binding type of m-Py-m GS to BSA. The synchronous fluorescence spectra state a mild effect of gemini surfactants on the emission intensity of tyrosine (Tyr) residues, on the other hand, tryptophan (Trp) residues showed a significant effect. Post addition of GS, the plot of pyrene fluorescence reveals the mild micropolarity fluctuations via the probe (pyrene) molecules encapsulated in BSA. UV-visible experiments support the complex formation between the BSA and m-Py-m GS. Far-UV CD measurements revealed the modifications in the secondary structure of protein produced by m-Py-m GS. Furthermore, we also used the computational molecular modeling for attaining deep insight into BSA and m-Py-m GS binding and the results are supported with our experimental results.

Discovery of a Pyrimidinedione Derivative with Potent Inhibitory Activity against Mycobacterium tuberculosis Ketol-Acid Reductoisomerase

New drugs aimed at novel targets are urgently needed to combat the increasing rate of drug-resistant tuberculosis (TB). Herein, the National Cancer Institute Developmental Therapeutic Program (NCI-DTP) chemical library was screened against a promising new target, ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid (BCAA) biosynthesis pathway. From this library, 6-hydroxy-2-methylthiazolo[4,5-d]pyrimidine-5,7(4H,6H)-dione (NSC116565) was identified as a potent time-dependent inhibitor of Mycobacterium tuberculosis (Mt) KARI with a K_i of 95.4 nm. Isothermal titration calorimetry studies showed that this inhibitor bound to MtKARI in the presence and absence of the cofactor, nicotinamide adenine dinucleotide phosphate (NADPH), which was confirmed by crystal structures of the compound in complex with closely related Staphylococcus aureus KARI. It is also shown that NSC116565 inhibits the growth of H37Ra and H37Rv strains of Mt with MIC₅₀ values of 2.93 and 6.06 μm, respectively. These results further validate KARI as a TB drug target and show that NSC116565 is a promising lead for anti-TB drug development.

Identification of tectoridin as the inhibitor of FTO by isothermal titration calorimetric and spectroscopic methods

The characteristics of binding between tectoridin and the fat mass and obesity-associated protein were investigated.

AtFKBP53: a chimeric histone chaperone with functional nucleoplasmin and PPIase domains

FKBP53 is one of the seven multi-domain FK506-binding proteins present in Arabidopsis thaliana, and it is known to get targeted to the nucleus. It has a conserved PPIase domain at the C-terminus and a highly charged N-terminal stretch, which has been reported to bind to histone H3 and perform the function of a histone chaperone. To better understand the molecular details of this PPIase with histone chaperoning activity, we have solved the crystal structures of its terminal domains and functionally characterized them. The C-terminal domain showed strong PPIase activity, no role in histone chaperoning and revealed a monomeric five-beta palm-like fold that wrapped over a helix, typical of an FK506-binding domain. The N-terminal domain had a pentameric nucleoplasmin-fold; making this the first report of a plant nucleoplasmin structure. Further characterization revealed the N-terminal nucleoplasmin domain to interact with H2A/H2B and H3/H4 histone oligomers, individually, as well as simultaneously, suggesting two different binding sites for H2A/H2B and H3/H4. The pentameric domain assists nucleosome assembly and forms a discrete complex with pre-formed nucleosomes; wherein two pentamers bind to a nucleosome.

Thermodynamics of inclusion within cyclodextrins and structural evidence of Cu(indomethacin)2 and Zn(indomethacin)2 complexes in aqueous solutions

Cu(IMC)₂ and Zn(IMC)₂ inclusion within cyclodextrins is spontaneous, the former driven by entropic and the last by enthalpic contributions.

Differential Scanning Calorimetry to Quantify Heat-Induced Aggregation in Concentrated Protein Solutions

Differential scanning calorimetry (DSC) is an important technique to measure the thermodynamics of protein unfolding (or folding). Information including the temperature for the onset of unfolding, the melt transition temperature (T_m), enthalpy of unfolding (ΔH), and refolding index (RI) are useful for evaluating the heat stability of proteins for a range of biochemical, structural biology, industrial, and pharmaceutical applications. We describe a procedure for careful sample preparation of proteins for DSC measurements and data analysis to determine a range of thermodynamic parameters. In particular, we highlight a measure of protein refolding following complete thermal denaturation (RI), which quantifies the proportion of protein lost to irreversible aggregation after thermal denaturation.

Binding interaction of sheep alpha-2-macroglobulin and tannic acid: A spectroscopic and thermodynamic study

Tannic acid is a polyphenol found in plant species commonly consumed by ruminants. It works as an important molecule in plant defense system to fight against environmental stressors. Tannic acid has number of effects on animals and humans. An attempt has been made to study the interaction of tannic acid with alpha-2-macroglobulin (α₂M). α₂M is a large tetrameric glycoprotein which function as a key serum anti-proteinase under physiological conditions. In the present study we explored the tannic acid-α₂M interaction by number of spectroscopic techniques such as UV, fluorescence, CD and FTIR along with isothermal titration calorimetry. CD and FT-IR spectroscopy were mainly used to study the secondary structural change induced in the antiproteinase. Analysis of activity shows the antiproteolytic potential of protein was compromised. Data of UV spectroscopy shows formation of α₂M-tannic acid complex. The thermodynamic signatures of this interaction reveals hydrogen bonding played a major role in the binding of α₂M-tannic acid. Analysis of CD and FTIR results suggest a minor conformational change in α₂M on tannic acid binding. Overall, tannic acid induces subtle conformation change in α₂M structure resulting the loss of its proteinase inhibitory activity.

Self-coacervation of modular squid beak proteins - a comparative study

The beak of the Humboldt squid is a biocomposite material made solely of organic components - chitin and proteins - which exhibits 200-fold stiffness and hardness gradients from the soft base to the exceptionally hard tip (rostrum). The outstanding mechanical properties of the squid beak are achieved via controlled hydration and impregnation of the chitin-based scaffold by protein coacervates. Molecular-based understanding of these proteins is essential to mimic the natural beak material. Here, we present detailed studies of two histidine-rich beak proteins (HBP-1 and -2) that play central roles during beak bio-fabrication. We show that both proteins have the ability to self-coacervate, which is governed intrinsically by the sequence modularity of their C-terminus and extrinsically by pH and ionic strength. We demonstrate that HBPs possess dynamic structures in solution and achieve maximum folding in the coacervate state, and propose that their self-coacervation is driven by hydrophobic interactions following charge neutralization through salt-screening. Finally, we show that subtle differences in the modular repeats of HBPs result in significant changes in the rheological response of the coacervates. This knowledge may be exploited to design self-coacervating polypeptides for a wide range of engineering and biomedical applications, for example bio-inspired composite materials, smart hydrogels and adhesives, and biomedical implants.

Thermodynamic cooperativity of cosubstrate binding and cation selectivity of Salmonella typhimurium MelB

The melibiose symporter MelB couples melibiose transport to that of cations such as Na⁺. Hariharan and Guan show that the binding of Na⁺ and melibiose is thermodynamically cooperative and that Na⁺ coupling is based on ion concentrations and competitive binding, but not ion selectivity.

The Na⁺-coupled melibiose symporter MelB, which can also be coupled to H⁺ or Li⁺ transport, is a prototype for the glycoside-pentoside-hexuronide:cation symporter family. Although the 3-D x-ray crystal structure of Salmonella typhimurium MelB (MelB_St) has been determined, the symport mechanisms for the obligatory coupled transport are not well understood. Here, we apply isothermal titration calorimetry to determine the energetics of Na⁺ and melibiose binding to MelB_St, as well as protonation of this transporter. Studies of the thermodynamic cycle for the formation of the Na⁺–MelB_St–melibiose ternary complex at pH 7.45 reveal that the binding of Na⁺ and melibiose is cooperative. The binding affinity for one substrate (Na⁺ or melibiose) is increased by the presence of the other by about eightfold. The coupling free energies (ΔΔG) of either substrate binding are ∼5 kJ/mol, and binding of both substrates releases a free energy of ∼35 kJ/mol. Measurements of the Na⁺-binding enthalpy at three different pH values, including the pK_a value of MelB, indicate that the binding of one Na⁺ displaces one H⁺ per MelB_St molecule. In addition, the absolute dissociation constants for Na⁺ and H⁺, determined by competitive binding, show that MelB_St is selective for H⁺ over Na⁺ by ∼1,000-fold at a pK_a of 6.25. Thus, the Na⁺ coupling in MelB_St is based not on ion selectivity but on ion concentrations and competitive binding because of a much higher Na⁺ concentration under physiological conditions. Such a selectivity feature seems to be common for membrane transport proteins that can bind both H⁺ and Na⁺ at a common site.

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches

Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico. All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats.

Molecular insight into the Grandivitin- matrix metalloproteinase 9 interactions

Grandivitin (GRA), a natural coumarin, can inhibit Matrix metalloproteinase 9 (MMP9). Binding characteristics are therefore of interest for pharmacodynamics of GRA and coumarin derivatives. A combination of spectroscopic methods and molecular modeling techniques was used to characterize interaction of GRA with MMP9. Fluorescence spectroscopy showed that GRA could quench the MMP9 fluorescence spectra. Changes in the UV-Vis and FT-IR spectra were observed upon ligand binding along with a significant degree of tryptophan fluorescence quenching on complex formation. Fluorescence studies showed that GRA has an ability to quench the intrinsic fluorescence of MMP9. Molecular modeling analysis showed that GRA to be bound in the large hydrophobic cavity of MMP9. Further investigation of the binding site of GRA within the MMP9 molecule suggested that hydrophobic contacts, hydrogen bond formation and electrostatic interactions account for the binding of GRA. According molecular dynamics (MD) simulation results the ligand can interact with the protein, with affecting the secondary structure of MMP9 and with a modification of its tertiary structure. The biological significance of this work is evident because MMP9 serves as a potential target protein for anticancer agents. The binding study of GRA with MMP9 is of great importance in pharmacy, pharmacology and biochemistry. This work can provide some key data to clinical research and supply the theoretical basis for the new drug candidate designing.

Multi-spectroscopic and molecular modeling investigation of the interactions between prantschimgin and matrix metalloproteinase 9 (MMP9)

The binding of prantschimgin (PRAN) to matrix metalloproteinase 9 (MMP9) was investigated using multiple techniques. Fluorescence spectroscopy showed that PRAN could quench the MMP9 fluorescence spectra. Changes in the UV/vis and Fourier transform infrared (FTIR) spectra were observed upon ligand binding, along with a significant degree of tryptophan fluorescence quenching on complex formation. The interaction of PRAN with MMP9 has also been studied using molecular docking and molecular dynamics (MD) simulation. The binding models demonstrated aspects of PRAN's conformation, active site interaction, important amino acids and hydrogen bonding. Computational mapping of the possible binding site of PRAN revealed that the ligand is bound in a large hydrophobic cavity of MMP9. The MD simulation results suggested that this ligand can interact with the protein, with little affecting the secondary structure. The results not only lead to a better understanding of interactions between PRAN and MMP9, but also provide useful data about the influence of PRAN on the structural conformation. The data provided in this study will be useful for designing a new agonist of MMP9 with the desired activity.

Combined spectroscopy and molecular modeling studies on the binding of galbanic acid and MMP9

The molecular mechanism of galbanic acid (GBA) binding to matrix metalloproteinase 9 (MMP9) was investigated by fluorescence quenching, absorption spectroscopy, FT-IR, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of MMP9 was quenched by GBA. The titration of MMP9 by various amount of GBA was also followed by UV-Vis absorption spectroscopy. The results revealed that GBA, as a biologically active sesquiterpene coumarin derivative, has an ability to bind strongly to MMP9. Molecular docking results indicated that the main active binding site for GBA has been located in a hydrophobic cavity in the vicinity of Zn atom. Moreover, MD simulation results suggested that GBA as a coumarin derivative can interact with MMP9, without affecting the secondary structure of MMP9. MD simulations, molecular docking as computational methods from one hand and experimental data from other hand reciprocally supported each other.

Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation

A method is proposed to study protein-ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide-protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated.

Extracting physics of life at the molecular level: A review of single-molecule data analyses

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.

A supramolecular approach to metal ion sensing: cystine-based designer systems for Cu2+, Hg2+, Cd2+ and Pb2+ sensing

Here, we demonstrate an emergent property from a mixture of two simple cystine containing molecules. The 1 : 1 mixture of pyrene-labelled S1 and tryptophan appended S2 form the heterodimeric system S1 : S2, which shows a unique metal binding ability.

Optimisation of isolation procedure for pyrrolizidine alkaloids from Rindera umbellata Bunge

Procedure for isolation of pyrrolizidine alkaloids (PAs) from Rindera umbellata Bunge plant species was optimised. Different extraction media (methanol, ethanol and sulphuric acid), concentration and volume of sulphuric acid, pH of PA solution for alkaline extraction, extraction time and techniques (maceration, ultrasonic and overhead rotary mixer assisted extraction) were investigated. The yields of six PAs (7-angeloyl heliotridane, 7-angeloyl heliotridine, lindelofine, 7-angeloyl rinderine, punctanecine and heliosupine) were monitored by GC-MS/FID. The best results for the isolation all of six PAs were obtained when the extraction was performed with 1 M sulphuric acid (30 mL per 1.00 g of dried sample) by overhead rotary mixer during three days. Optimal pH value for alkaline extraction of PAs with CH₂Cl₂ was 9, and the extraction should be performed with four portions of 30 mL of CH₂Cl₂. This procedure could be also useful for a plant sample preparation for GC and LC analyses of PAs.

Thermodynamics of binding of structurally similar ligands to histone deacetylase 8 sheds light on challenges in the rational design of potent and isozyme-selective inhibitors of the enzyme

Among the different histone deacetylase (HDAC) isozymes, HDAC8 is the most highly malleable enzyme, and it exhibits the potential to accommodate structurally diverse ligands (albeit with moderate binding affinities) in its active site pocket. To probe the molecular basis of this feature, we performed detailed thermodynamic studies of the binding of structurally similar ligands, which differed with respect to the “cap”, “linker”, and “metal-binding” regions of the suberoylanilide hydroxamic acid (SAHA) pharmacophore, to HDAC8. The experimental data revealed that although the enthalpic (ΔH°) and entropic (ΔS°) changes for the binding of individual SAHA analogues to HDAC8 were substantially different, their binding free energies (ΔG°) were markedly similar, conforming to a strong enthalpy–entropy compensation effect. This effect was further observed in the temperature-dependent thermodynamics of binding of all SAHA analogues to the enzyme. Notably, in contrast to other metalloenzymes, our isothermal titration calorimetry experiments (performed in different buffers of varying ionization enthalpies) suggest that depending on the ligand, its zinc-binding group may or may not be deprotonated upon the binding to HDAC8. Furthermore, the heat capacity changes (ΔC_p°) associated with the ligand binding to HDAC8 markedly differed from one SAHA analogue to the other, and such features could primarily be rationalized in light of the dynamic flexibility in the enzyme structure in conjunction with the reorganization of the active site resident water molecules. Arguments are presented that although the binding thermodynamic features described above would facilitate identification of weak to moderately tight-binding HDAC8 inhibitors (by a high-throughput and/or virtual screening of libraries of small molecules), they would pose major challenges for the structure-based rational design of highly potent and isozyme-selective inhibitors of human HDAC8.

Diversity of Pyrrolizidine Alkaloids in the Boraginaceae Structures, Distribution, and Biological Properties

Among the diversity of secondary metabolites which are produced by plants as means of defence against herbivores and microbes, pyrrolizidine alkaloids (PAs) are common in Boraginaceae, Asteraceae and some other plant families. Pyrrolizidine alkaloids are infamous as toxic compounds which can alkylate DNA und thus cause mutations and even cancer in herbivores and humans. Almost all genera of the family Boraginaceae synthesize and store this type of alkaloids. This review reports the available information on the present status (literature up to early 2014) of the pyrrolizidine alkaloids in the Boraginaceae and summarizes the topics structure, distribution, chemistry, chemotaxonomic significance, and biological properties.

Cysteine-based fluorescence “turn-on” sensors for Cu2+ and Ag+

Amino acid cysteine was transformed to fluorescent turn-on sensors for Cu⁺² and Ag⁺. The metal ion binding was studied in detail by spectroscopic, microscopic, calorimetric and computational methods.